MetaboNews Masthead
Published in partnership between
TMIC and the Metabolomics Society
Issue 40 - December 2014

CONTENTS:


Online version of this newsletter:
http://www.metabonews.ca/Dec2014/MetaboNews_Dec2014.htm

Welcome to the fortieth issue of MetaboNews, a monthly newsletter published in partnership between The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/) and the international Metabolomics Society (http://www.metabolomicssociety.org/), to keep metabolomics researchers and other professionals informed about new technologies, software, databases, events, job postings, conferences, training opportunities, interviews, publications, awards, and other newsworthy items concerning metabolomics. MetaboNews represents the one-stop-shop for the very latest and most critical news about the science of metabolomics. In this issue, we feature a Metabolomics Spotlight article on nmrML, a vendor-neutral open exchange format for NMR-based metabolomics, and a metabolomics interview with Alex Buko of Human Metabolome Technologies.
This issue of MetaboNews is supported by:

Metanomics Health
     
Chenomx -- Metabolite Discovery & Measurement
Metanomics Health GmbH
Chenomx Inc.

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Metabolomics Society Logo

Metabolomics Society News


CONFERENCE CORNER

11th Annual International Conference of the Metabolomics Society
Location: San Francisco, USA
Date: June 29 - July 2, 2015
Website: http://metabolomics2015.org/

New Members-only benefit: Are you organizing a metabolomics event?
The Metabolomics Society can provide small grants to support events that promote metabolomics. The funding may be used to provide student prizes, travel awards or catering for small events such as symposia, workshops, seminars and short-courses. The Society may also sponsor larger conferences where there is strategic opportunity to promote metabolomics science within other scientific disciplines. For more information, or to apply for funding, see: http://metabolomicssociety.org/index.php/events/event-funding

The Society has recently sponsored a keynote address at the Colorado Biological MS Society Fall Meeting, and assisted with catering for the Merlion Metabolomics Workshop in Singapore. Both were highly successful events and demonstrated the growth of metabolomics in these regions.

3rd Annual Practical Applications of NMR in Industry Conference (PANIC)
The Metabolomics Society is providing one travel award for an Early-Career member of the Society to attend PANIC 2015. Apply via the PANIC website by 15th December.
Location: La Jolla, CA, USA
Date: February 9 - 12, 2015
Website: http://www.panicnmr.com/ 


MEMBERS CORNER

Early-career Members Network (EMN)
The EMN is dedicated to and run by early-career scientists who are members of the Metabolomics Society and are from academia, government, or industry. The network aims to provide a forum for metabolomics researchers at the start of their professional career.

The EMN is planning to establish a series of online webinars. These sessions will range from very basic requirements across our discipline to more dedicated sessions with top scientists in metabolomics. The first webinar is planned for early 2015. Watch this space for more details!

Please feel free to contact us via info.emn@metabolomicssociety.org if you have suggestions for our online webinars. Furthermore, we are hoping to receive comments on our planned activities and additional ideas for activities that the EMN could organize. The EMN can only be a success with your support and ideas!

Membership renewal for 2015 now available!
Membership of the Society is based on the calendar year and this year’s membership will end December 31st 2014. All current members will need to renew their membership to stay in good standing. You can renew your membership now for 2015 here. Remember to renew early to take advantage of our early bird discounted registration fees. Join now and save some money!

We hope that you have enjoyed being part of and benefitted from the considerable expansion of the Metabolomics Society during the past few years, and will remain a loyal member of our growing community. As the society continues to expand, we expect to be able to offer further membership benefits including discounted member registration at the 11th Annual Metabolomics Society Conference in San Francisco. Student members and Early Career members with over 3 months standing are also able to apply for our Student Prize and Travel Awards. These provide considerable financial support to allow students and early career researchers to attend several conferences events and workshops including:
 Member benefits:
  1. No membership fee increases for 2015.
  2. Networking and information exchange with an international membership of professionals devoted to furthering metabolomics related science: via conferences and workshops, the Society’s many Interest Groups, and social media including the Society’s Facebook page and Twitter feed.
  3. Discounted registration fees for Metabolomics Society conferences.
  4. Subscription for electronic access (and optional print copies*) to the Metabolomics journal, the official publication of the Society.
  5. Receive information and electronic notices of metabolomics conferences, workshops and seminars.
  6. Posting of job advertisements on the Society's website and via Twitter.
  7. Automatic delivery of the joint Metabolomics Society/The Metabolomics Innovation Center (TMIC) MetaboNews newsletter with the latest news from the metabolomics world.
  8. Eligibility to nominate individuals for an Honorary Fellowship of the Society** and to vote in Society elections.
  9. Eligibility to stand for Office within the Society**.
  10. Eligibility to apply for travel awards and prizes.
* Additional fee applies, see registration website; Members will also have electronic access to all issues and therefore print copies of back issues will not be available to Members who register late in the calendar year.
** Not applicable for Student Members.


TASK GROUPS CORNER

Metabolite Identification Task Group
The Metabolite Identification Task Group currently works with ten members who are focused on discussing reporting standards for metabolite identification; see the opinion paper in publications corner for a recent publication from the task group. As developments unfold we will keep all informed. Furthermore, we are working to link the Natural Products community to the Metabolomics community in this area; congratulations to Stefano Caldarelli who recently hosted near Paris over 100 attendees on the first (of hopefully) many workshops dedicated to this integration of communities.


INTERNATIONAL AFFILIATES CORNER

Australian & New Zealand Metabolomics Network (ANZMN)
Visit http://www.anzmn.com.au

This month the ANZMN would like to congratulate team member Dr. Darren Creek (interviewed in last month’s MetaboNews) for his recent grant success with the Australian National Health and Medical Research Council (NHMRC). In a tough round Darren managed to get not one but two grants; a Career Development Fellowship (4 years) and a 3-year project grant investigating metabolism in African trypanosomes. Darren was also part of another successful grant that will involve using metabolomics for drug discovery (see http://www.creek-lab.com for details). Reading the list of funded NHMRC grants there appear to be quite a few that have metabolomics/lipidomics aspects, so Australia continues its impressive run of form funding metabolomics research.

Metabolomics Australia and the ANZMN also jointly ran a very successful beginners workshop at the end of October with attendees from Australia, New Zealand and Canada attending lectures in the morning and getting their hands dirty in the lab running samples in the afternoon. Feedback has been universally positive and thanks are due to everybody involved at both the ANZMN and Metabolomics Australia for a job well done.

Finally the ANZMN would like to wish everybody all the best for the Christmas holiday season and all the best for a successful new year in 2015.


PUBLICATIONS CORNER

Metabolomics journal, Vol. 10, Issue 6, December 2014
See the latest issue of our journal at: http://link.springer.com/journal/11306/10/6/page/1

In addition to the many excellent research papers, this issue contains the following contributions on the Metabolomics Society pages:
 Stay abreast of the latest metabolomics news via the Twitter feed on the front page of the website. Also you can follow us on Twitter: Metabolomics Society @MetabolomicsSoc and Metabolomics journal @Metabolomics. And you can visit us on Facebook.


OTHER FEATURES

Invitation for nominations for Honorary Fellows for 2015
Nominations for Honorary Fellows for 2015 are now open with a deadline by the 1st of February, 2015 (http://metabolomicssociety.org/index.php/awards/honorary-fellowships)

Nominees shall be recognized as having made outstanding contributions to the Metabolomics Society and shall be know as pioneers and contributors to the metabolomics sciences either in the technological developments, computational biology or to the application of metabolomics to a specific scientific area. Please email your nominations to nominations@metabolomicssociety.org.

HAPPY HOLIDAYS
Last but not least, we wish our members and metabolomics friends a wonderful seasonal break and all the very best for 2015!
 
Software Spotlight

Metabolomics Spotlight

 nmrML Logo
 COSMOS Logo

nmrML: A vendor-neutral open exchange format for NMR-based metabolomics

Feature article contributed by Daniel Schober, Michael Wilson, Daniel Jacob, Annick Moing, Catherine Deborde, Kenneth Haug, Philippe Rocca-Serra, John Easton, Tim Ebbels, Jie Hao, Christian Ludwig, Antonio Rosato, David Wishart, Christoph Steinbeck, Reza Salek, Steffen Neumann, and the COSMOS standards developers

Metabolomics is a growing field and the number of organisms being studied is constantly increasing as is the number of metabolites being discovered. With this growth comes a steady increase in the amount of metabolomics data and the need to ensure that we capture this information in persistent open formats and databases.

The COSMOS project (COordination Of Standards In MetabOlomicS, http://www.cosmos-fp7.eu/) has been created to improve the adoption of open standards for metabolomics data, annotation with agreed metadata, and support by open source data management and capturing tools. COSMOS delivers an ecosystem of formats, tools, and resources such as MetaboLights (http://www.ebi.ac.uk/metabolights/), a database for capturing information obtained in metabolomics experiments.

Here we introduce recent developments in nmrML (www.nmrml.org), a vendor-neutral open exchange and storage format to describe NMR-based metabolomics data (Figure 1). Currently, the most widely used open source data exchange format for NMR data is JCAMP-DX (Joint Committee on Atomic and Molecular Physical Data [1]). While many tools exist that make use of JCAMP-DX, the specification has several issues, mostly related to the fact that its specification is not very rigorous, which leads to difficulties to validate a data file and interoperability problems between software implementations. These issues motivated the creation of the nmrML specification.

To ensure the needs of the metabolomics community are met by the format, we relied on detailed suggestions about the minimum information (MI) metadata to be captured for an NMR experiment, developed by the Metabolomics Standards Initiative (MSI) working groups [2]. The MSI herein put forth recommendations to report instrument descriptions and configurations, instrument-specific sample preparation, and data acquisition parameters [3].

Click on the thumbnail below to view a larger version of the image

Illustration of NMR data management facilitation by means of nmrML

Figure 1. Illustration of NMR data management facilitation by means of nmrML.

We were also heavily inspired by the mzML [4] specification that has been widely adopted in mass spectrometry. The format consists of an XML schema that defines the structure of an nmrML file and a supporting controlled vocabulary (nmrCV). This separation keeps the XML structure simple and avoids frequent changes of the schema when the terminology needs to accommodate new technologies and parameters. This also allows for the reuse of nmrCV in other formats and tools. The development of nmrML takes place on Github (https://github.com/nmrML/nmrml), where the specification documents, more detailed descriptions of our use cases, examples files, and parser libraries can be found. The current nmrML release is available at http://nmrml.org for public consultation and feedback.

Several implementations in reusable software libraries are available, e.g., for Java and Python, to convert from Bruker or Agilent/Varian to the nmrML format on the command line or through a web application (Figure 2).

Click on the thumbnail below to see a larger version of the image

Java-based nmrML converter

Figure 2. The Java-based nmrML converter allows uploaded Bruker or Varian raw data NMR files (FID and parameter files) to be converted into a valid nmrML file (inset).

A semantic validation web service allows nmrML files to be checked for schema conformance and annotation compliance, thus contributing to quality assurance, by assessing data completeness against established MI checklists, e.g., the minimal information for a metabolomics NMR experiment [3].

We provide parser libraries for nmrML in R and Matlab, which can be used by open NMR processing and analysis software. The nmrRIO R package for example aims at providing a common interface to several R-based NMR packages such as BATMAN [5] and rNMR [6]. The Matlab nmrML parser reads nmrML parameters and decodes FID and spectrum array data, which can then be visualized.

nmrML is an important step forward in the openness, reusability, and reproducibility of metabolomics NMR experiments. Creating nmrML, we have focused on the needs of the metabolomics community, and worked with partners and users throughout the creation process to ensure that we are meeting their specific requirements and use cases. We are already working with several partners who have adopted formats such as MetaboLights (http://www.ebi.ac.uk/metabolights/) and HMDB (http://hmdb.ca/), and we have seeded the beginning of an ecosystem of tools and software around nmrML. Help us to grow the nmrML community by using the tools and contributing your work or suggestions at http://nmrml.org.


References
  1. Davies A.N. and Lampen P. (1993) JCAMP-DX for NMR. Appl. Spec., 47, 1093-1099. http://www.jcamp-dx.org/
  2. Sansone S.A., Fan T., Goodacre R. et al. (2007) The metabolomics standards initiative. Nat. Biotechnol., 25, 846–848.
  3. Rubtsov D.V., Jenkins H., Ludwig C., Easton J., Viant M.R., Günther U., Griffin J.L., Hardy N. (2007) Proposed reporting requirements for the description of NMR-based metabolomics experiments. Metabolomics 3, 223–229.
  4. Martens L., Chambers M., Sturm M. et al. (2011) mzML—a community standard for mass spectrometry data. Mol. Cell Proteomics, 10, R110000133. [PMID: 20716697]
  5. Hao J. et al. (2012) BATMAN--an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model. Bioinformatics, 28(15), 2088-90. [PMID: 22635605]
  6. Lewis I. A., Schommer S.C., Markley J.L. (2009)  rNMR: open source software for identifying and quantifying metabolites in NMR spectra. Magn Reson Chem, 47 Suppl 1, S123-126. doi:10.1002/mrc.2526. [PMID: 19821464]

Please note: If you know of any metabolomics research programs, software, databases, statistical methods, meetings, workshops, or training sessions that we should feature in future issues of this newsletter, please email Ian Forsythe at metabolomics.innovation@gmail.com.

 MetaboInterview Icon

MetaboInterviews
MetaboInterviews features interviews with prominent researchers in the field of metabolomics. The aim of these interviews is to shed light on metabolomics researchers around the world and give them an opportunity to share their metabolomics story. In this issue, we feature an interview with Alex Buko.


Vice President, Business and Product Development, Human Metabolome Technologies, Boston, USA
Alex Buko
Biography

I received my Bachelor’s degree in 1975 from University of Virginia in Geochemistry and a PhD in 1980 from University of Virginia in Chemistry developing mass spectrometric sequencing of proteins. From 1980 to 1984, I completed a post-doctoral fellowship at the FDA Bureau of Biologics and Biophysics, studying sequencing of inflammatory cytokines and natriuretic factors in blood. I worked at Abbott Laboratories in Chicago from 1984 to 2002, and led a large lab analyzing small molecules, metabolites, and proteins. I worked on measuring metabolites using MALDI-TOF and experimented with capillary electrophoresis mass spectrometry (CE-MS) for proteins and small molecules, using MALDI-FTMS and LC-MS/MS.

I moved to Biogen Idec from 2002 to 2012 and led a large lab analyzing small molecules, proteins, and antibodies. I built proteomic and metabolic platforms at both Abbott and Biogen Idec. Over the course of my career, I have worked on disease and drug response biomarkers in several therapeutic areas and believe in a systems biology approach using innovative data mining tools with algorithm generation.

Currently I am VP of Business and Product Development at Human Metabolome Technologies. Our company has been delivering quantitative and non-quantitative CE-MS metabolic profiles for many years mainly in Japan. Metabolomics and metabolite profiling have experienced significant growth in the US and Europe over the past several years covering many areas of science. Since HMT has developed an extensive metabolite database over the past 10 years, serving many areas from agriculture to pharmaceuticals, the time has come to bring HMT metabolomics to a growing US market.

Metabolomics Interview (MN, MetaboNews; AB, Alex Buko)

MN: How did you get involved in metabolomics?

AB: In the early days of biological mass spectrometry (1985-1995), we were using LC-MS and high resolution MS to identify and characterize active metabolites and natural products (small molecules) in combination with NMR from plant and soil extracts. We did not call it metabolomics back then, more like natural product identification. However, the analytical process was similar to today: Extraction of metabolites followed by analysis and identification. Instead of looking at all extractables, we were focused on only those with biological activity. Seeing the need for better sensitivity and resolution, we used CE-MS to look at small extractables in drug formulations and plant extracts. However, the sensitivity and reproducibility of those early hybrid techniques seem primitive to what can be done today using high resolution chromatography and high accuracy mass spectrometry. Later as the techniques improved and databases expanded, we started adding metabolites to our proteomics data sets to add specificity and opportunity to our biomarker discovery data analysis.

 MN: What are some of the most exciting aspects of your work in metabolomics?

AB: Currently I am working as VP Business and Product Development for Human Metabolome Technologies (HMT), a Japanese-based contract research organization (CRO) using CE-MS and LC-MS for targeted and untargeted metabolomic profiling. After spending 28 years in Pharma/Biotech, I am seeing the world from another angle bringing my pharmaceutical experiences to a diagnostic and biomarker discovery organization. Their advances using CE-MS over what I had done 20 years ago demonstrates the advances in technology that has allowed metabolomics to expand and grow. At HMT I am combining my knowledge of the drug industry to the CRO workplace to enable and enhance communications, expectations, deliverables and product development, while learning about work flow efficiencies, pricing and marketing strategies. Within this business, I am also expanding my knowledge beyond pharmaceutical research to other industries such as agriculture, nutrition, and other disease areas outside my prior work.

 MN: What key metabolomics initiatives are you pursuing at your research centre or institute?

AB: We all see the need for quantitative analysis in comparing analytes across multiple sample cohorts. In the post genomic world, discovery starts out with quantitative methods using RT-qPCR and GWAS or antibody and aptamer-based assays, while proteomics, metabolomics and lipidomics (others…) generally start out with relative measurements, unless there is a testable hypothesis to run a quantitative assay for a specific protein or metabolite.

At HMT we are looking to bring quantitation closer to unbiased discovery to increase the degree of accuracy and comparability across discovery sets that include 100s of samples, analyzed over months. Our unbiased metabolite profiling platforms BasicScan and AdvancedScan offer our clients to quantitate 100 metabolites in the same data set as the relative profiling data. CE also allows for the observation and quantitation of many polar metabolites that are not observed well or at all using reverse-phase liquid chromatography (RPLC) methods. Our LC-MS option adds up to 300 lipids to complete our profiling. Using multiple internal standards, high resolution capillary electrophoresis and quantitation, we look to demonstrate data of highly quality and transferability that ultimately would show fewer false positives yet with broad coverage of the metabolome. While our CARCINOSCOPE™ panel of 116 central energy metabolites offers discovery with quantitation, F-SCOPE offers up to 54 metabolites quantified using isotope flux analysis. Technical improvements, however, cannot do all the work. Inclusive and comprehensive study design, growing metabolite databases and multi-variant analysis will also need to be involved to solve the complex questions we face using clinical trial patient populations.

 MN: What is happening in your country in terms of metabolomics?

AB: There is slow and steady growth in the field as seen by the growth and funding of NIH centers and University/Medical Research core facilities. Publications in the area are steadily climbing. Investor-sponsored research portfolios continue to project double digit growth over the next several years. At the same time, big data initiatives are growing.

However, there has been growing talk about the non-reproducibility of scientific data in the literature. There are questions about whether metabolomics data is quantitatively good enough for early biomarker discovery or robust enough for discovery in blood. The scientific community is looking for success in metabolomics, as they have questioned genomic and proteomics data in the past. What is necessary for success when choosing to add metabolomic data is to understand the differences between labs and technology platforms. Not all metabolomic labs and methods have the same capabilities, advantages, and disadvantages. The list of known metabolites is growing as the techniques we use continue to improve and expand. Metabolomics is an enabling technology, but also a maturing area.

MN: How do you see your work in metabolomics being applied today or in the future?

AB: I am a firm believer in a systems biology approach to biomarker discovery and pathway analysis. While there are always opportunities that individual biomarkers of one flavor (miRNA, Protein, autoantibody, Metabolite) can be found, there are limited number of successes using a single platform focus when looking for biomarkers for disease progression or therapeutic intervention. Using quantitative and comprehensive metabolomics in combination with clinical data and other measurable data to create multi-analyte algorithms may be the future of predictive medicine.

MN: As you see it, what are metabolomics' greatest strengths?

AB: Bringing to point of care, the clinical assay development process takes a lot of time and money to show specificity, selectivity, and demonstrate biological context. Creating a robust metabolite assay can be faster, cheaper, and better for multiplex quantitative assays than protein assays using monoclonal antibodies. In addition, metabolomics has the capability of adding critical data to complex analyses using mRNA and protein expression to increase the specificity of pathway analysis. Much is also known about metabolic pathways adding to the biological interpretation of results. Lastly, metabolites can provide accurate readouts of complex biological processes and be conveniently measured in clinical samples such as blood, urine, or saliva.

 MN: What do you see as the greatest barriers for metabolomics?

AB: Despite all the success already in this field, there are several areas of improvement, hence metabolomics is still a developing technology. Creating a sensitive and robust assay for a single targeted metabolite is doable today, however, the bigger hurdles are in the discovery process. We would like to expand the number of metabolites we can measure in one analysis without adding more platforms. Sensitivity can always be improved to dig deeper into the metabolome. High mass accuracy to help identify new metabolites is good today, but the process of identification and verification of new metabolites can be difficult, expensive, and time consuming. Dealing with large concentration ranges without serial dilutions would be more cost and time efficient.

 MN: What improvements, technological or otherwise, need to take place for metabolomics to really take off?

AB: As with other omics data, success is catching. We need to see more downstream validation of early discovery and more examples of bringing metabolic data from discovery to the clinic. To expand metabolomic analysis we need to lower the costs for discovery, reduce sample volume requirements, and increase the accuracy and depth of metabolomic analysis.

 MN: How does the future look in terms of funding for metabolomics?

AB: The challenge for all science today is funding, whether academic or the industrial laboratory. The NIH has spurred success with their funding of NIH metabolomic facilities. Many research organizations have provided subsidy funding for core metabolomic labs. How long these funding streams can continue to help provide lower cost analysis is unclear. DNA sequencing costs were driven down by technology improvements, large scale needs, and the perceived criticality of the data. However, metabolomics will unlikely be driven by a single platform to capture such molecular heterogeneity and the criticality of the data has not yet been demonstrated. Hence, providing lower cost analysis will continue to be a struggle.

 MN: What role can metabolomics standards play?

AB: I see two types of standards. There are validated reference standards of individual metabolites stored under conditions to preserve the integrity of the sample. The analogy may be ATCC cell lines, antibody repositories and protein/peptide standards. To create a new metabolomics platform and to build a current platform, having the availability of standards is critical to validate new metabolites in your platform and to build quantitative assays. A second type of standard would be a biological standard such as the NIST SRM 1950 plasma standard. This standard has been qualified using several techniques and could provide a basis to pressure test new platforms or quality control samples to test platform consistency.

 MN: Do you have any other comments that you wish to share about metabolomics?

AB: As I said earlier, metabolomics continues to be an enabling and developing technology with applications in all areas of research, from primary cell lines to point of care clinical measurements, in many areas of study from Alzheimer’s to Oncology, and in many application areas from Pharmaceuticals to Agriculture. Most platforms today are agnostic to sample type or area of application. The size and identity of the metabolome will change from serum to tissue to plant extracts. However, with proper extraction protocols, increasing metabolite databases and improving technologies, metabolomic research is making a significant contribution to science and medicine.

Please note: We are open to suggestions for our MetaboInterviews section. Please send suggestions for future interview candidates to Ian Forsythe at metabolomics.innovation@gmail.com.
Metabolomics Current Contents

Metabolomics Current Contents

Recently published papers in metabolomics:


MetaboNews

MetaboNews
19 Nov 2014
Patients to benefit from new £5m MRC Regional Phenome Centre at the University of Birmingham, UK

The University of Birmingham, UK, has announced plans to establish a £5m MRC Regional Phenome Centre (RPC), which will help to improve the health of patients through novel research and technology. The centre will complement and work closely with the MRC-NIHR National Phenome Centre in London. It will help scientists to better detect the onset of several diseases and to develop more effective treatments, focusing primarily on patients with immune-mediated inflammatory diseases and blood cancers. Significant improvements in patient health, as well as cost savings to the UK’s National Health Service, are anticipated through early detection and tailoring of treatment.

The centre will be led by Professor Mark Viant, Professor Ulrich Guenther and Dr Warwick Dunn. Building on existing metabolomics technologies in the Schools of Biosciences and Cancer Sciences at the University of Birmingham, the MRC award will fund ten additional mass spectrometers and NMR spectrometers to greatly enhance the number of samples that can be investigated. The centre will soon be recruiting six full-time metabolomics scientists, applying LC-MS, NMR spectroscopy and computational biology. The first of these six posts, the Operational Head of Mass Spectrometry and Bioinformatics for the MRC RPC, is currently being advertised (see the Metabolomics Jobs section below).

The metabolomics research at Birmingham and the new centre benefit from an existing Technology Alliance Partnership between the University of Birmingham and Thermo Fisher Scientific for advancing life sciences mass spectrometry, and a technology collaboration between the University and Beckman Coulter for advancing automation solutions in the omics sciences. Collaborations with Bruker and Waters will further enhance the capacity and capabilities of the centre.

Professor Viant said, “We are tremendously excited about building a metabolomics facility of the scale needed to significantly improve our ability to understand mechanisms of human disease and improve treatments. The centre will provide the UK with a significant advantage that we will exploit to generate new diagnostic and prognostic biomarkers of both common and rare diseases.”

National Phenome Centre Director, Professor Jeremy Nicholson of Imperial College London, added, “We are pleased to be associated with the new MRC Regional Phenome Centre at Birmingham and this will form part of a wider network of national and regional centres that will harmonise with the NPC and the linked Imperial BRC Clinical Phenome Centre. The multiple benefits of network driven commonalities of approach, methodology, data mining and database generation are easy for all to see."

The MRC RPC will form a cornerstone of the new £25m Institute for Translational Medicine, which will open in June 2015 and is governed through the Birmingham Health Partners, a strategic alliance between the University of Birmingham, University Hospitals Birmingham NHS Foundation Trust and Birmingham Children’s Hospital.

Professor David Adams, Dean of Medicine at the University of Birmingham and Director of Birmingham Health Partners commented, “These are exciting new technologies that we anticipate with bring significant patient benefits, both locally and nationally.”

About the National Phenome Centre
 The MRC-NIHR National Phenome Center is a partnership between Imperial College London and Kings College London with Waters Corporation and Bruker Biospin. Opened in July 2013 under the Directorship of Professor Jeremy Nicholson of Imperial College (http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/newssummary/news_4-6-2013-12-3-42), the NPC provides the world's first national capability and capacity for large scale metabolic phenotyping for molecular epidemiology biomarker studies and stratified medicine programs using a multiple high field NMR and mass spectrometer cluster. For further information visit http://www1.imperial.ac.uk/phenomecentre/
5 Nov 2014
Steno opens new metabolomics laboratory

Steno Diabetes Center has today officially opened its new state-of-the-art metabolomics laboratory. The goal of the new technology is bringing Steno at the forefront of personalized diabetes treatment.

"The overall goal is to bring metabolomics technology into the clinic," says Matej Orešič, principal investigator of Systems Medicine at the Steno Diabetes Center. "The new technology will enable us to predict the development of the disease, which can guide health professionals in relation to establishing personalized prevention and treatment of diabetes."

Metabolomics is a field of research that examines metabolites in fluids, tissues and cells. Metabolites such as glucose and cholesterol, have been extensively studied in diabetes research, while the current metabolomics technology makes it possible to examine thousands of metabolites simultaneously.

Until now, metabolomics technology primarily been used in research projects, but has now become so developed that it can be used in clinical practice.

"Based on a metabolomics analysis, we will hopefully be able to provide a profile of the patient and predict the risk of diabetes and diabetes complications, and the patient's response to a specific therapy. The challenge is to translate the detailed information from more than 1000 metabolites into useful information for clinical practice. It requires much training and is an interesting and relevant area to develop, "says Tuulia Hyötyläinen, head of the new metabolomics laboratory.

Steno laboratory contains several instruments that provide detailed analyzes of polar metabolites and lipids, as well as quantitative analyzes of selected groups of metabolites.

The new equipment is already in use in several research projects are underway in Systems Medicine research group has recently been established at Steno. The plan for metabolomics laboratory is to start with research projects and so involve patients from Steno's clinic in 3-4 months when all clinical validations are in place.

"I want to congratulate Matej Orešič and Tuulia Hyötyläinen to have established their laboratory so soon after their employment at Steno," says Managing. Director John Nolan.
"The new metabolomics and lipidomics laboratory is a significant step forward for the Steno Diabetes Center and will strengthen our capacity for translational research in the early development of diabetes and prevention. We look forward to establishing new collaborations with colleagues in Denmark and internationally. "

Steno Diabetes Center is one of the first diabetes clinics in the world where one implements metabolomics in clinical practice.

Many partners from the Danish diabetes research community attended the opening, which took place at the Steno Diabetes Center's birthday, established November 5, 1932.

Source: Press Release translated into English (Google Translate)
Original Press Release (in Danish)


Metabolomics Events

Metabolomics Events
3-5 Dec 2014

2nd Australian Lipid Meeting
Venue: University of Wollongong (Innovation Campus), Wollongong, NSW, Australia

We are pleased to announce the 2nd Australian Lipid Meeting, which will be held at the University of Wollongong's Innovation Campus from 3-5 December, 2014.

While the first meeting focused on lipidomics we have expanded the scope for the second meeting to cover all aspects of lipid research. Planned topics include:
  • Imaging
  • Botany
  • Nutrition
  • Health and Disease
  • Technical Developments and Methodology
We look forward to seeing you in "The Gong".

Registration
  • Open: 1 August, 2014
  • Early bird: Closes 28 October, 2014
For further details, please see the event flyer or visit http://ihmri.uow.edu.au/research-program/australianlipidsmeeting/index.html
11 Dec 2014

London Biological Mass Spectrometry Discussion Group
Venue: Cancer Research UK, 44 Lincoln's Inn Fields, London, WC2A 3LY, UK

The meeting will be held at Cancer Research UK, 44 Lincoln's Inn Fields, London, WC2A 3LY.  The nearest tubes are Holborn or Chancery Lane.
 
A change to the normal course of events is that this meeting will start at 13:30 with a buffet lunch.  We are grateful to our sponsors of this meeting, Shimadzu, which enables us to offer the meetings as free to attend.  If you plan on coming it would be helpful if you could send an email to: lbmsdg2006@gmail.com

To see the agenda for this event, click here.
11-13 Dec 2014

2nd ICAN (Institute of Cardiometabolism and Nutrition) Conference Series 2014
Venue: St James and Albany Hotel, Paris, France
Diabetes, obesity, and heart diseases

Further Information: http://ican-series.com/
Registration: https://www.etouches.com/ereg/newreg.php?eventid=97217&
Download the Flyer.

For further details, visit the conference website.
9-12 Feb 2015

3rd Annual Practical Applications of NMR in Industry Conference (PANIC)
Venue: La Jolla, CA, USA

You are invited to attend Practical Applications of NMR in Industry Conference (PANIC), February 9 – 12, 2015 in La Jolla, CA.  Students are encouraged to apply for travel awards, and the Metabolomics Society has sponsored one award (free registration) that is exclusively available to Early-Career Members of the Metabolomics Society!

The PANIC meeting is intended to address topics that occur daily in industrial, government, and academic research laboratories whose primary task entails the application of NMR to a diverse set of analytical problems. Topics include quantitation, molecular structure characterization, trace component and mixture analysis, and product support for a variety of materials that include small molecules, polymers, heterogeneous mixtures, natural products, biosimilars, polysaccharides, and proteins. The conference provides in-depth discussions of the “nuts and bolts” of basic NMR experiments that accent the underlying best-practices developed to address these everyday problems. It also explores the regulatory aspects of the applications of these experiments.

Greater insights will be provided into the less frequently explored techniques used in NMR such as quantitation, chemometrics, automation, relaxometry, and at/on line instrumentation. Attendees will have the opportunity to learn about and discuss applications of NMR to polymers, petroleum, food, agriculture, and nutritional supplements that are rarely discussed at other NMR meetings. Ample opportunity will be given to Network with people who are experts in inventing NMR experiments to solve real world problems in a timely and efficient manner that is demanded by working in the venue of product delivery.

For more details, visit http://www.panicnmr.com.
16-20 Feb 2015

EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists
Venue: European Bioinformatics Institute, CB10 1SD, United Kingdom (Google Maps)

Organizers

Participation: Open application with selection

Course overview
This course will provide an overview of key issues that affect metabolomics studies, handling dataset and procedures for the analysis of metabolomics data using bioinformatics tools. It will be delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course will provide a platform for discussion of the key questions and challenges in the field of metabolomics, from study design to metabolite identification.

Audience
This course is aimed at PhD students, post-docs and researchers with at least two or three year’s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis. Participants ideally must have working experience using R (including a basic understanding of the syntax and ability to manipulate objects).

For more details, visit http://www.ebi.ac.uk/training/course/metabolomics2015.
28 Mar to 1 Apr 2015

Plant Metabolism Session at the ASBMB Annual Meeting
Venue: Boston, Massachusetts

Plant Metabolism will be a 4 day-session at the ASBMB meeting: http://www.asbmb.org/meeting2015/ and http://www.asbmb.org/meetings/annualmeeting2015/sessions/themes/plant/

The abstract submission site is open and accepting abstracts at http://www.asbmb.org/meetings/annualmeeting2015/abstracts/instructions/

Short talks will be chosen from the submitted abstracts. Volunteered abstract submission deadline is THURSDAY, NOVEMBER 6, 2014 (a strict deadline for short talk programming consideration). Plant Metabolism abstracts should be submitted using ASBMB Abstract Topic Categories # 2350 – 2360.

For more information, click here and visit http://www.asbmb.org/meetings/annualmeeting2015/sessions/themes/plant/.
29 Jun to 2 Jul 2015

Metabolomics 2015: 11th Annual Conference of the International Metabolomics Society
The Official Annual Meeting of the International Metabolomics Society
Location: San Francisco, USA
Venue: Hyatt Regency, Burlingame, USA

You are invited to join us for Metabolomics 2015, the official annual meeting of the Metabolomics Society.

This stunning world-class venue will host the most exciting metabolomics conference of 2015. Your host institution, the University of California, Davis, will gladly welcome scientists from all around the world to feel at home and relax while hearing of the latest innovations and breakthroughs in metabolomics.

Please see the Open Call for Organization of Workshops

Stay abreast of the latest Metabolomics Society news via the Twitter feed on the front page of the website (http://www.metabolomicssociety.org). Also you can follow us on Twitter: Metabolomics Society @MetabolomicsSoc and Metabolomics journal @Metabolomics. And you can visit us on Facebook.
For further details, visit http://metabolomics2015.org.

Please note: If you know of any metabolomics lectures, meetings, workshops, or training sessions that we should feature in future issues of this newsletter, please email Ian Forsythe (metabolomics.innovation@gmail.com).

Metabolomics Jobs

Metabolomics Jobs

This is a resource for advertising positions in metabolomics. If you have a job you would like posted in this newsletter, please email Ian Forsythe (metabolomics.innovation@gmail.com). Job postings will be carried for a maximum of 4 issues (8 weeks) unless the position is filled prior to that date.

Jobs Offered

Job Title Employer Location Posted Closes Source
Research Fellow (Parasitology/Metabolomics)
 Monash University
 Parkville, Victoria, Australia 27-Nov-2014
 18-Dec-2014
 SEEK
Postdoctoral Researcher in Metabolomics of Cancer
 Karolinska Institutet
 Stockholm, Sweden 27-Nov-2014
 31-Jan-2015
 Karolinska Institutet
Operational Head of Mass Spectrometry and Bioinformatics at the MRC Regional Phenome Centre University of Birmingham Birmingham, UK 19-Nov-2014
 9-Dec-2014
 University of Birmingham
Masters Student - The Science of Adductomics: Application to Gestational Diabetes
 Liggins Institute, University of Auckland
 Auckland, New Zealand 14-Oct-2014
 14-Dec-2014
 Metabolomics Society Jobs
PhD Studentship
 International Pregnancy Research Alliance (IPRA)
 Chongqing, China 27-Aug-2014
 31-Dec-2014
 Metabolomics Society Jobs
Mass Spectrometry Technician International Pregnancy Research Alliance (IPRA) Chongqing, China 27-Aug-2014 31-Dec-2014 Metabolomics Society Jobs


Jobs Wanted

This section is intended for very highly qualified individuals (e.g., lab managers, professors, directors, executives with extensive experience) who are seeking employment in metabolomics. We encourage these individuals to submit their position requests to Ian Forsythe (metabolomics.innovation@gmail.com). Upon review, a limited number of job submissions will be selected for publication in the Jobs Wanted section.
  • Postdoctoral position in an international metabolomics research group where I will be able to gain valuable experience in all aspects of metabolomics to eventually be able to get my own group going: [Candidate's CV] [Candidate's LinkedIn Profile]


Equipment

  • For Sale (ex-lease equipment): Waters Synapt G2 Mass Spectrometer (2010), including 3 months warranty by Waters.
    Including:
    • LockSpray Source with ESI probe
    • NanoLockSpray with Universal sprayer
    • MaxEnt V4.1
    • Transform V4.1
    • Mass Lynx v4.1
    • Available with Ion Mobility Upgrade if required
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